Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016545.1 Corchorus olitorius cultivar O-4 contig16578, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40206
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--47 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 ATCTAC
7 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48 CAAGTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7654 original size:25 final size:24
Alignment explanation
Indices: 7626--7687 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
7616 GTGGATTGTA
*
7626 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
7651 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
*
7675 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
7688 TTGACCCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 9 0.26
24 8 0.24
25 17 0.50
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:8555 original size:93 final size:93
Alignment explanation
Indices: 8457--8694 Score: 386
Period size: 93 Copynumber: 2.5 Consensus size: 93
8447 AATAGGTATA
8457 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
1 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
8522 AAGTATAATTAAATAGTTATAAGGATAT
66 AAGTATAATTAAATAGTTATAAGGATAT
8550 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
1 TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
8615 AAGTATAATTAAATAGTTATAAGGATAT
66 AAGTATAATTAAATAGTTATAAGGATAT
*
8643 TAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
1 T--A---AA-T--A-AAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGT
8695 TTAAATAATG
Statistics
Matches: 135, Mismatches: 1, Indels: 9
0.93 0.01 0.06
Matches are distributed among these distances:
93 94 0.70
95 1 0.01
98 2 0.01
99 1 0.01
101 1 0.01
102 36 0.27
ACGTcount: A:0.51, C:0.02, G:0.11, T:0.37
Consensus pattern (93 bp):
TAAATAAAAAATAGAGTTTTTATTTGAGTAAAACTATAAAAGTATATTTAAAAATTCTAATATAA
AAGTATAATTAAATAGTTATAAGGATAT
Found at i:8826 original size:11 final size:11
Alignment explanation
Indices: 8810--8841 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
8800 TGTACTTTTA
8810 TATATATATAG
1 TATATATATAG
8821 TATATATATAG
1 TATATATATAG
*
8832 TATAGATATA
1 TATATATATA
8842 TATTTTCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (11 bp):
TATATATATAG
Found at i:13181 original size:24 final size:24
Alignment explanation
Indices: 13153--13200 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
13143 TGAAAAAAAA
13153 AAAGTTGAGATTATAAGTGAAATC
1 AAAGTTGAGATTATAAGTGAAATC
13177 AAAGTTGAGATTATAAGTGAAATC
1 AAAGTTGAGATTATAAGTGAAATC
13201 TTATTGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAGTTGAGATTATAAGTGAAATC
Found at i:13648 original size:17 final size:17
Alignment explanation
Indices: 13623--13656 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13613 GGGGAGAGAC
* *
13623 AATAGAATATGGAGAAG
1 AATAAAATATGAAGAAG
13640 AATAAAATATGAAGAAG
1 AATAAAATATGAAGAAG
13657 GGGAGAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (17 bp):
AATAAAATATGAAGAAG
Found at i:20002 original size:1 final size:1
Alignment explanation
Indices: 19996--20034 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
19986 ATTGGCAATC
*
19996 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20035 GGCCGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:20259 original size:27 final size:26
Alignment explanation
Indices: 20221--20282 Score: 101
Period size: 24 Copynumber: 2.4 Consensus size: 26
20211 ATGACTATAA
20221 GACTTCCTCTTTTTTTTTTTTTTAAAG
1 GACTTCCTC-TTTTTTTTTTTTTAAAG
20248 GACTTCCTC--TTTTTTTTTTTAAAG
1 GACTTCCTCTTTTTTTTTTTTTAAAG
20272 GACTTCCTCTT
1 GACTTCCTCTT
20283 CAAGTGTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 24 0.73
27 9 0.27
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (26 bp):
GACTTCCTCTTTTTTTTTTTTTAAAG
Found at i:26130 original size:5 final size:5
Alignment explanation
Indices: 26120--26144 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26110 TGCATCTTTT
26120 ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA
26145 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTTA
Done.